--- Comment #2 from ---
The problem was probably extrawiki's DB setup with a separate flowdb on the

$ mysql flowdb
(21:28) root@localhost:[flowdb]> source
extensions/Flow/db_patches/patch-remove_usernames.sqlQuery OK, 10 rows affected
(0.56 sec)

then rerun maintenance/update.php

This seems hard to fix unless there's some magic comment that will use
$wgFlowExternalStore and $wgFlowDefaultWikiDb to target the right cluster.

BTW the FlowSetUserIp script doesn't output anything, there's no indication
when it successfully runs

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